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WASHINGTON - The House overwhelmingly passed a $649 billion defense spending bill yesterday that boosts the Pentagon budget by $17 billion and covers the costs of wars in Iraq and Afghanistan.

The strong bipartisan vote was 336 to 87 and reflected lawmakers’ intent to ensure national security, preserve defense jobs across the nation, and avoid deep cuts while the country is at war.

While House Republican leaders slashed billions from all other government agencies, the Defense Department is the only one that will see a double-digit increase in its budget beginning Oct. 1.

Amid negotiations to cut spending and raise the nation’s borrowing limit, the House rejected several amendments to cut the Pentagon budget, including a measure by Representative Barney Frank, a Newton Democrat, to halve the bill’s increase in defense spending.

“We are at a time of austerity,’’ Frank said. “We are at a time when the important programs, valid programs, are being cut back.’’

Scoffing at the suggestion that “everything is on the table’’ in budget negotiations between the Obama administration and congressional leaders, Frank said, “The military budget is not on the table. The military is at the table, and it is eating everybody else’s lunch.’’

Still, the overall bill is $9 billion less than President Obama sought.

The White House has threatened a veto, citing limits on the president’s authority to transfer detainees from the US prison at Guantanamo Bay, Cuba, and money for defense programs it did not want.

The measure includes $119 billion for the wars in Iraq and Afghanistan.

The House also voted to slow repeal of the policy allowing gays to serve openly in the military, backing an amendment to block funds for the training manual for the Chaplain Corps on ending the “don’t ask, don’t tell’’ policy.

Representative Tim Huelskamp, Republican of Kansas, sponsor of the amendment, said its purpose was to prohibit chaplains from performing same-sex marriages on Navy bases regardless of a state’s law. The House approved the measure 236 to 184.

The vote was one of several steps the Republican-controlled chamber has taken this year to delay implementation of Obama’s new policy.

Pentagon leaders have said they see no roadblocks to ending the 17-year ban, and Defense Secretary Leon Panetta is likely to certify the change for midsummer after military training ends.

“What will happen to chaplains who decline to officiate over same-sex ceremonies?’’ Huelskamp asked. “The directive states that chaplains ‘may’ perform same-sex civil marriage ceremonies. I fear that chaplains who refuse to perform these ceremonies may find themselves under attack and their careers threatened.’’

Separately, a federal appeals court in California this week ordered the US government to cease enforcing the ban immediately on openly gay members of the military.